SEXP _reported_matches_asSEXP()
{
SEXP start, width, ans;
switch (internal_match_buf.ms_code) {
case MATCHES_AS_NULL:
return R_NilValue;
case MATCHES_AS_COUNTS:
case MATCHES_AS_WHICH:
return ScalarInteger(_get_match_count());
case MATCHES_AS_RANGES:
PROTECT(start = new_INTEGER_from_IntAE(
internal_match_buf.match_starts->elts[active_PSpair_id]));
PROTECT(width = new_INTEGER_from_IntAE(
internal_match_buf.match_widths->elts[active_PSpair_id]));
PROTECT(ans = new_IRanges("IRanges", start, width, R_NilValue));
UNPROTECT(3);
return ans;
}
error("Biostrings internal error in _reported_matches_asSEXP(): "
"invalid 'internal_match_buf.ms_code' value %d",
internal_match_buf.ms_code);
return R_NilValue;
}
/* --- .Call ENTRY POINT --- */
SEXP BWGFile_query(SEXP r_filename, SEXP r_ranges, SEXP r_return_score,
SEXP r_return_list) {
pushRHandlers();
struct bbiFile * file = bigWigFileOpen((char *)CHAR(asChar(r_filename)));
SEXP chromNames = getAttrib(r_ranges, R_NamesSymbol);
int nchroms = length(r_ranges);
Rboolean return_list = asLogical(r_return_list);
SEXP rangesList, rangesListEls, dataFrameList, dataFrameListEls, ans;
SEXP numericListEls;
bool returnScore = asLogical(r_return_score);
const char *var_names[] = { "score", "" };
struct lm *lm = lmInit(0);
struct bbiInterval *hits = NULL;
struct bbiInterval *qhits = NULL;
if (return_list) {
int n_ranges = 0;
for(int i = 0; i < nchroms; i++) {
SEXP localRanges = VECTOR_ELT(r_ranges, i);
n_ranges += get_IRanges_length(localRanges);
}
PROTECT(numericListEls = allocVector(VECSXP, n_ranges));
} else {
PROTECT(rangesListEls = allocVector(VECSXP, nchroms));
setAttrib(rangesListEls, R_NamesSymbol, chromNames);
PROTECT(dataFrameListEls = allocVector(VECSXP, nchroms));
setAttrib(dataFrameListEls, R_NamesSymbol, chromNames);
}
int elt_len = 0;
for (int i = 0; i < nchroms; i++) {
SEXP localRanges = VECTOR_ELT(r_ranges, i);
int nranges = get_IRanges_length(localRanges);
int *start = INTEGER(get_IRanges_start(localRanges));
int *width = INTEGER(get_IRanges_width(localRanges));
for (int j = 0; j < nranges; j++) {
struct bbiInterval *queryHits =
bigWigIntervalQuery(file, (char *)CHAR(STRING_ELT(chromNames, i)),
start[j] - 1, start[j] - 1 + width[j], lm);
/* IntegerList */
if (return_list) {
qhits = queryHits;
int nqhits = slCount(queryHits);
SEXP ans_numeric;
PROTECT(ans_numeric = allocVector(REALSXP, width[j]));
memset(REAL(ans_numeric), 0, sizeof(double) * width[j]);
for (int k = 0; k < nqhits; k++, qhits = qhits->next) {
for (int l = qhits->start; l < qhits->end; l++)
REAL(ans_numeric)[(l - start[j] + 1)] = qhits->val;
}
SET_VECTOR_ELT(numericListEls, elt_len, ans_numeric);
elt_len++;
UNPROTECT(1);
}
slReverse(&queryHits);
hits = slCat(queryHits, hits);
}
/* RangedData */
if (!return_list) {
int nhits = slCount(hits);
slReverse(&hits);
SEXP ans_start, ans_width, ans_score, ans_score_l;
PROTECT(ans_start = allocVector(INTSXP, nhits));
PROTECT(ans_width = allocVector(INTSXP, nhits));
if (returnScore) {
PROTECT(ans_score_l = mkNamed(VECSXP, var_names));
ans_score = allocVector(REALSXP, nhits);
SET_VECTOR_ELT(ans_score_l, 0, ans_score);
} else {
PROTECT(ans_score_l = mkNamed(VECSXP, var_names + 1));
}
for (int j = 0; j < nhits; j++, hits = hits->next) {
INTEGER(ans_start)[j] = hits->start + 1;
INTEGER(ans_width)[j] = hits->end - hits->start;
if (returnScore)
REAL(ans_score)[j] = hits->val;
}
SET_VECTOR_ELT(rangesListEls, i,
new_IRanges("IRanges", ans_start, ans_width, R_NilValue));
SET_VECTOR_ELT(dataFrameListEls, i,
new_DataFrame("DataFrame", ans_score_l, R_NilValue,
ScalarInteger(nhits)));
UNPROTECT(3);
}
}
bbiFileClose(&file);
if (return_list) {
ans = new_SimpleList("SimpleList", numericListEls);
UNPROTECT(1);
} else {
PROTECT(dataFrameList =
new_SimpleList("SimpleSplitDataFrameList", dataFrameListEls));
PROTECT(rangesList = new_SimpleList("SimpleRangesList", rangesListEls));
ans = new_RangedData("RangedData", rangesList, dataFrameList);
UNPROTECT(4);
}
lmCleanup(&lm);
popRHandlers();
return ans;
}
